Force fields in GROMACS

AMBER

AMBER (Assisted Model Building and Energy Refinement) refers both to a set of molecular mechanical force fields for the simulation of biomolecules and a package of molecular simulation programs.

GROMACS versions higher than 4.5 support the following AMBER force fields natively:

  • AMBER94
  • AMBER96
  • AMBER99
  • AMBER99SB
  • AMBER99SB-ILDN
  • AMBER03
  • AMBERGS

Information concerning the force field can be found using the following information:

  • AMBER Force Fields - background about the AMBER force fields
  • AMBER Programs - information about the AMBER suite of programs for molecular simulation
  • ANTECHAMBER/GAFF - Generalized Amber Force Field (GAFF) which is supposed to provide parameters suitable for small molecules that are compatible with the AMBER protein/nucleic acid force fields. It is available either together with AMBER, or through the antechamber package, which is also distributed separately. There are scripts available for converting AMBER systems (set up, for example, with GAFF) to GROMACS (amb2gmx.pl, or acpypi.py), but they do require an AMBER installation to work.

Older GROMACS versions need a separate installation of the ffamber ports:

  • Using AMBER Force Field in GROMACS - known as the “ffamber ports,” a number of AMBER force fields, complete with documentation.
  • Using the ffamber ports with GROMACS requires that the input structure files adhere to the AMBER nomenclature for residues. Problematic residues involve termini (prefixed with N and C), lysine (either LYN or LYP), histidine (HID, HIE, or HIS), and cysteine (CYN or CYX). Please see the ffamber documentation.

CHARMM

CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a both a set of force fields and a software package for molecular dynamics simulations and analysis. Includes united atom (CHARMM19) and all atom (CHARMM22, CHARMM27, CHARMM36) force fields. The CHARMM27 force field has been ported to GROMACS and is officially supported as of version 4.5. CHARMM36 force field files can be obtained from the MacKerell lab website, which regularly produces up-to-date CHARMM force field files in GROMACS format.

For using CHARMM36 in GROMACS 5.0 and newer, please use the following settings in the mdp file:

constraints = h-bonds
cutoff-scheme = Verlet
vdwtype = cutoff
vdw-modifier = force-switch
rlist = 1.2
rvdw = 1.2
rvdw-switch = 1.0
coulombtype = PME
rcoulomb = 1.2
DispCorr = no

Note that dispersion correction should be applied in the case of lipid monolayers, but not bilayers.

Please also note that the switching distance is a matter of some debate in lipid bilayer simulations, and it is dependent to some extent on the nature of the lipid. Some studies have found that an 0.8-1.0 nm switch is appropriate, others argue 0.8-1.2 nm is best, and yet others stand by 1.0-1.2 nm. The user is cautioned to thoroughly investigate the force field literature for their chosen lipid(s) before beginning a simulation!

Anyone using very old versions of GROMACS may find this script useful:

CHARMM to GROMACS - perl scripts intended to facilitate calculations using GROMACS programs and CHARMM forcefields (needed for GROMACS versions < 4.5). (link)

GROMOS

GROMOS is is a general-purpose molecular dynamics computer simulation package for the study of biomolecular systems. It also incorporates its own force field covering proteins, nucleotides, sugars etc. and can be applied to chemical and physical systems ranging from glasses and liquid crystals, to polymers and crystals and solutions of biomolecules.

GROMACS supports the GROMOS force fields, with all parameters provided in the distribution for 43a1, 43a2, 45a3, 53a5, 53a6 and 54a7. The GROMOS force fields are united atom force fields, i.e. without explicit aliphatic (non-polar) hydrogens.

  • GROMOS 53a6 - in GROMACS format (J. Comput. Chem. 2004 vol. 25 (13): 1656-1676).
  • GROMOS 53a5 - in GROMACS format (J. Comput. Chem. 2004 vol. 25 (13): 1656-1676).
  • GROMOS 43a1p - 43a1 modified to contain SEP (phosphoserine), TPO (phosphothreonine), and PTR (phosphotyrosine) (all PO42- forms), and SEPH, TPOH, PTRH (PO4H- forms).

OPLS

OPLS (Optimized Potential for Liquid Simulations) is a set of force fields developed by Prof. William L. Jorgensen for condensed phase simulations, with the latest version being OPLS-AA/M.

The standard implementations for those force fields are the BOSS and MCPRO programs developed by the Jorgensen group

As there is no central web-page to point to, the user is advised to consult the original literature for the united atom (OPLS-UA) and all atom (OPLS-AA) force fields, as well as the Jorgensen group page